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Past Issues in 2015

Volume: 5 Issue: 10

Cancer Biology

Genome-Wide siRNA Screen for Anti-Cancer Drug Resistance in Adherent Cell Lines Authors: Elza C. de Bruin, Ming Jiang, Michael Howell and Julian Downward, date: 05/20/2015, view: 10016, Q&A: 0

The expression of genes is frequently manipulated in cell lines to study their cellular functions. The use of exogenous small Interfering RNAs (siRNAs) is a very efficient technique to temporarily downregulate the expression of genes of interest [reviewed by Hannon and Rossi (2004)]. A genome-wide siRNA library allows the user to study both the ...

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Proximity Ligation Assay (PLA) to Detect Protein-protein Interactions in Breast Cancer Cells Authors: Mike Z Lin, Janet L Martin and Robert C Baxter, date: 05/20/2015, view: 25573, Q&A: 0

Protein-protein interaction networks provide a global picture of cellular function and biological processes, and the dysfunction of some interactions causes many diseases, including cancer. The in situ proximity ligation assay (PLA) is a powerful technology capable of detecting the interactions among proteins in fixed tissue and cell ...

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Immunology

Murine Liver Myeloid Cell Isolation Protocol Authors: Benoit Stijlemans, Amanda Sparkes, Chloé Abels, Jiri Keirsse, Lea Brys, Yvon Elkrim, Patrick De Baetselier, Alain Beschin and Jo A Van Ginderachter, date: 05/20/2015, view: 26102, Q&A: 3

In homeostasis, the liver is critical for the metabolism of nutrients including sugars, lipids, proteins and iron, for the clearance of toxins, and to induce immune tolerance to gut-derived antigens. These functions predispose the liver to infection by blood-borne pathogens, and to a variety of diseases ranging from toxin and medication-induced ...

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Isolation of Particles of Recombinant ASC and NLRP3 Authors: Fátima Martín-Sánchez, Ana I. Gómez and Pablo Pelegrín, date: 05/20/2015, view: 9465, Q&A: 0

NLRP3 inflammasome is a multiprotein complex responsible for the activation of inflammatory caspase-1, resulting in processing and release of pro-inflammatory cytoquines IL-1β and IL-18 (Schroder and Tschopp, 2010). This inflammasome is composed of the sensor protein NLRP3 connected to caspase-1 through the adaptor protein ASC ...

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Microbiology

Determining the Relative Fitness Score of Mutant Viruses in a Population Using Illumina Paired-end Sequencing and Regression Analysis Authors: Hangfei Qi, C. Anders Olson, Nicholas C. Wu, Yushen Du and Ren Sun, date: 05/20/2015, view: 6826, Q&A: 0

Recent advances in DNA sequencing capacity to accurately quantify the copy number of individual variants in a large and diverse population allows in parallel determination of the phenotypic effects caused by each genetic modification. This systematic profiling approach is a combination of forward and reverse genetics, which we refer to as ...

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Human, Bacterial and Fungal Amplicon Collection and Processing for Sequencing Author: Julia Oh, date: 05/20/2015, view: 9998, Q&A: 3

Sequencing taxonomic marker genes is a powerful tool to interrogate the composition of microbial communities. For example, bacterial and fungal community composition can be evaluated in parallel using the 16S ribosomal RNA gene for bacteria or the internal transcribed spacer region in fungi. These are conserved regions that are universal to a ...

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Molecular Biology

RNA-binding Protein Immunoprecipitation (RIP) to Examine AUF1 Binding to Senescence-Associated Secretory Phenotype (SASP) Factor mRNA Authors: Elise Alspach and Sheila A. Stewart, date: 05/20/2015, view: 11530, Q&A: 0

Immunoprecipitation and subsequent isolation of nucleic acids allows for the investigation of protein:nucleic acid interactions. RNA-binding protein immunoprecipitation (RIP) is used for the analysis of protein interactions with mRNA. Combining RIP with quantitative real-time PCR (qRT-PCR) further enhances the RIP technique by allowing for the ...

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Plant Science

Histochemical Detection of Zn in Plant Tissues Authors: Ilya Seregin, Anna Kozhevnikova and Henk Schat, date: 05/20/2015, view: 8076, Q&A: 0

Accumulation of metals in plant tissues, and occasionally, different cells of the same tissue, may be highly non-uniform (Seregin and Kozhevnikova, 2008). Easy-to-use histochemical methods may greatly help to investigate the distribution and accumulation of metals within and among plant tissues, and also provide information on their subcellular ...

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Fluorescence-based CAPS Multiplex Genotyping on Capillary Electrophoresis Systems Authors: Jelena Perovic, Cristina Silvar, Dragan Perovic, Nils Stein and Frank Ordon, date: 05/20/2015, view: 7540, Q&A: 0

Recent advances in next-generation sequencing techniques allow the detection of a large number of SNPs and their use in a high throughput manner. However, Cleaved Amplified Polymorphic Sequences (CAPSs) still play a significant role as complement to other high throughput methods for SNP genotyping. Therefore, new methods focusing on the ...

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Pyrosequencing Approach for SNP Genotyping in Plants Using a M13 Biotinylated Primer Authors: Cristina Silvar, Dragan Perovic, Anna M Casas, Ernesto Igartua and Frank Ordon, date: 05/20/2015, view: 7986, Q&A: 0

Single Nucleotide Polymorphisms (SNPs), which constitute single base-pair variations in the DNA sequence, are the most abundant molecular markers in plant and animal genomes. They are becoming the markers of choice for genotyping in all fields of molecular biology, as they are easily prone to automation and high throughput, for example through ...

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Transient Transformation of Artemisia annua Authors: Dongming Ma and Hong Wang, date: 05/20/2015, view: 6347, Q&A: 0

Transient transformation of Artemisia annua does not depend on chromosomal integration of heterologous DNA, and recombinant DNA can be introduced into plant cells via Agrobacterium aided by vacuum. The leaves of 7th and 8th internode from 4-week-old seedlings were chosen as explants, a vacuum system was applied to facilitate ...

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Plant Materials and Growth Conditions of Japanese Morning Glory (Ipomoea nil cv. Violet) Author: Kenichi Shibuya, date: 05/20/2015, view: 8659, Q&A: 0

Japanese morning glory (Ipomoea nil) is a summer annual vine that typically produces ephemeral flowers. This plant has been used extensively to investigate flowers, including studies on flowering, flower color, and petal senescence. Here we describe the materials and optimal growth conditions used to grow the Japanese morning glory ...

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Establishment of a Symbiotic in vitro System between a Green Meadow Orchid and a Rhizoctonia-like Fungus Authors: Enrico Ercole, Michele Rodda, Mariangela Girlanda and Silvia Perotto, date: 05/20/2015, view: 9145, Q&A: 0

Symbiotic orchid seed germination in an in vitro system allows the growth of mycorrhizal protocorms and plantlets for scientific purposes. Orchids in nature need to establish a mycorrhizal symbiosis with fungal partners to germinate and develop into adult plants. Here we present a protocol for symbiotic germination of the terrestrial ...

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Measurement of Mitochondrial Respiration Rate in Maize (Zea mays) Leaves Authors: Xiao-Min Wang, Ning Chang, Yu-Rong Bi and Bao-Cai Tan, date: 05/20/2015, view: 6610, Q&A: 0

Mitochondria play essential roles in plant growth and development as they host the oxidative phosphorylation pathways, tricarboxylic acid cycle and other important metabolisms. Disruption of mitochondrial functions frequently leads to embryo lethality. Moreover, mitochondria play roles in programmed cell death, pathogen and stress responses in ...

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